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A new view of #SpeciesConcepts by @JeannettWhitton and me, clarifying time frames while unifying interbreeding, genealogy, and traits. A general-purpose species should be a reproductive community (bound by cohesive processes) viewed retrospectively (RRCC). doi.org/10.18061/bssb.…

PhD Using bees🐝, bee microbes 🦠& state-of-the-art automated bioreactors to drive the 🧬evolution of beneficial traits in bee microbial communities then explore how persistent they are in the face of competition & stress. Focus: evolution, microbiome engineering & metabolomics

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We expanded kallisto to translated alignment (nucleotides <-> amino acids), and used it to detect novel viruses in RNA seq data. The single-cell resolution allowed us to determine whether the presence of these viruses affected host gene expression. 🧵 biorxiv.org/content/10.110…

What is purpose of Literature Review?

We look for a motivated PhD student at U.Greifswald for a joint project with NHM Stuttgart and me at Museum Koenig also involved. Phylogenetics & species delimitation of New Caledonian freshwater snails uni-greifswald.de/en/university/…

Check it out and let us know what you think. Thanks to my many co-authors, including @jessthorpemas Dr. Sabrina Simon Dr. Akito Kawahara Scott Hotaling Lars Podsiadlowski Alex Donath and many others! Merry Christmas!

That time all your favorite devs teamed up to write a book about coding. And all the royalties went to Amnesty International. Brian Kernighan, Simon Peyton Jones, Bryan Cantrill, Greg Koah-Hartman, Jeff Dean, R. Kent Dybvig, Yukihiro Matsumoto, what a list.

Say Goodbye to Expensive Software! Here are 10 websites that can replace hundreds of dollars worth of PC software (for free)! [🔖Bookmark for the future]

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) peerj.com/articles/16505/ PeerJ Publishing

Friends don't let friends make bad charts! Chenxin Li, pulled together a lot of great advice for data visualization, with clear "do this, not that" examples for each item. Here are a few of my favorites, see the link below for more.

added a couple more tools including odp, ModDotPlot, and trackplot (python version)

#Pangenome graphs improve the analysis of SVs for rare genetic diseases. Our new study is out! Great collaboration with the lab of Tomi Pastinen and congrats to Cristian Groza @[email protected] for the amazing work! nature.com/articles/s4146…

BCFtools/liftover: bcftools plugin to convert genetic variants across genome assemblies academic.oup.com/bioinformatics… 🧬🖥️ github.com/freeseek/score…

Now you can use it as an R package. Generates a comprehensive EDA report in minutes. github.com/gexijin/inspect

Generating chain files to liftover annotations from one assembly to another can be real a pain. `transanno` is a nice tool that works with minimap2 to do this easily: github.com/informationsea…

Rust is already taking over bioinformatics with high quality tools. #itshappening

I’m so proud of this work! Awesome collaboration between Galaxy Project and Vertebrate Genomes Project (VGP) to make reference quality genomes accessible for all. 51 (!!!) new vertebrate genomes presented here means only about 70,000 left to go😀🚀

Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement (October 2023) nature.com/articles/s4146… 🧬🖥️ github.com/JiaoLaboratory…

Jointly benchmarking small and structural variant calls with vcfdist biorxiv.org/content/10.110… 🧬🖥️ github.com/TimD1/vcfdist